I looked again and I have exactly the same equipment as you (speakers, converter, amp and sub). I did another install in a Traverse a while back and used infinity components, alpine sub and 2 kenwood amps and got it sounding great but wanted to minimize space I went the 5 channel amp like you in the focus). I did set the output levels on the converter like they showed on their website (I have frt, rear, and sub all in the same position as I'm not sure how to set them independently using the 'maximize' light on converter...I have them all between 2/3 and 3/4 and I believe you do). I have the crossovers in the front components set to the middle (0) position.
I'll mess around with the amp gains and set the rear to be less than fronts to see if that helps. I did some adjustments and got it sounding pretty good but one thing is for sure...the sound quality definitely depends on the source (ipod and CD sound best by far, Sirius depends on the channel as does the local radio...wish they would all broadcast the same quality and equilized signal).
I've been messing around with the bass adjustments on the converter and found a good balance with the level set just under the midpoint and the Accubass at about 1/4 (and output level at ~2/3 as mentioned above).
Please do let me know what your amp gains are set at for front/rear/sub if you don't mind.
Couple other questions please:
1) I have the remote-in on the converter tied into the antenna wire but I notice the power light lights (and on the amp naturally since linked to converter) when I open the doors (before I turn the car on and/or radio on). I thought it woudn't engage until the radio is powered on). What did you end up doing on this.
2) I also get the on/off thumb in the sub before I turn on the radio as well (probably for same reason noted in #1)...have you solved this issue?